Contents
| Samples | OTUs | OTU Total Count | OTU Table Density |
|---|---|---|---|
| 215 | 3136 | 3635209.0 | 0.10828191741813004 |
This occurs de novo during clustering using the UCHIME algorithm and as reference-based on the OTU seed sequences against Unite version 7 database
Counts observed per sample as represented in the biom file (file1). This count is representative of quality filtered reads that were assigned per sample to OTU seed sequences.
| Minimum Count | Maximum Count | Median | Mean | Standard Deviation |
|---|---|---|---|---|
| 1.0 | 33490.0 | 16880.0 | 16907.9488372 | 5967.62496189 |
Taxonomy was assigned to the OTU sequences at an overall cutoff of 0.8%.
Taxonomy database - Unite version 7 database
Reads were quality filtered with BBDuk2 [3] to remove adapter sequences and PhiX with matching kmer length of 31 bp at a hamming distance of 1. Reads shorter than 51 bp were discarded. Reads were merged using USEARCH [4] with a minimum length threshold of 175 bp and maximum error rate of 1%. Sequences were dereplicated (minimum sequence abundance of 2) and clustered using the distance-based, greedy clustering method of USEARCH [5] at 97% pairwise sequence identity among operational taxonomic unit (OTU) member sequences. De novo prediction of chimeric sequences was performed using USEARCH during clustering. Taxonomy was assigned to OTU sequences using BLAST [6] alignments followed by least common ancestor assignments across Unite version 7 database [7]. OTU seed sequences were filtered against Unite version 7 database [8] to identify chimeric OTUs using USEARCH.
More files are available in relation to this analysis than are presented here. They can be accessed from the results directory and are organized by your experiment ID (wattenburger-job2-its/97):
wattenburger-job2-its/97/ # clustering pairwise identity threshold
├── blast
│ ├── blast_hits.txt # raw blast hits per OTU seed seq
│ ├── lca_assignments.txt # raw lca results TSV from blast hits
│ ├── OTU.biom # tax annotated biom (no metadata, no normalization)
│ ├── OTU_tax.fasta # otu seqs with tax in FASTA header
│ ├── OTU.txt # tab delimited otu table with taxonomy
│ └── README.html # results report when annotation method is 'blast'
├── logs
│ ├── cluster_sequences.log
│ ├── fasttree.log
│ └── uniques.log
├── OTU_aligned.fasta # multiple alignment file of otu seed seqs
├── OTU.fasta # otu seqs without taxonomy
├── OTU.tree # newick tree of multiple alignment
├── utax
│ ├── OTU.biom # tax annotated biom (no metadata, no normalization)
│ ├── OTU_tax.fasta # otu seqs with tax in FASTA header
│ ├── OTU.txt # tab delimited otu table with taxonomy
│ ├── README.html # results report when annotation method is 'utax'
│ └── utax_hits.txt # raw UTAX hits per OTU seed seq
├── demux
│ ├── *.fastq.count
│ └── *.fastq
├── logs
│ ├── quality_filtering_stats.txt
│ └── *.count
├── merged_?.fasta # error corrected FASTA prior to clustering into OTU seqs
├── merged.fastq # all sample reads merged into single file with updated headers
└── quality_filter
└── *.fastq # files that should have been cleaned up!